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  • American Geophysical Union (AGU)
  • Annual Reviews
  • 2015-2019  (793)
  • 1980-1984
  • 1935-1939
  • 2019  (793)
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  • 2015-2019  (793)
  • 1980-1984
  • 1935-1939
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  • 1
    Publication Date: 2019-04-29
    Description: Over 100 whole-genome sequences from algae are published or soon to be published. The rapidly increasing availability of these fundamental resources is changing how we understand one of the most diverse, complex, and understudied groups of photosynthetic eukaryotes. Genome sequences provide a window into the functional potential of individual algae, with phylogenomics and functional genomics as tools for contextualizing and transferring knowledge from reference organisms into less well-characterized systems. Remarkably, over half of the proteins encoded by algal genomes are of unknown function, highlighting the volume of functional capabilities yet to be discovered. In this review, we provide an overview of publicly available algal genomes, their associated protein inventories, and their quality, with a summary of the statuses of protein function understanding and predictions.
    Print ISSN: 1543-5008
    Electronic ISSN: 1545-2123
    Topics: Biology
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  • 2
    Publication Date: 2019-04-29
    Description: When exposed to warmer, nonstressful average temperatures, some plant organs grow and develop at a faster rate without affecting their final dimensions. Other plant organs show specific changes in morphology or development in a response termed thermomorphogenesis. Selected coding and noncoding RNA, chromatin features, alternative splicing variants, and signaling proteins change their abundance, localization, and/or intrinsic activity to mediate thermomorphogenesis. Temperature, light, and circadian clock cues are integrated to impinge on the level or signaling of hormones such as auxin, brassinosteroids, and gibberellins. The light receptor phytochrome B (phyB) is a temperature sensor, and the phyB–PHYTOCHROME-INTERACTING FACTOR 4 (PIF4)–auxin module is only one thread in a complex network that governs temperature sensitivity. Thermomorphogenesis offers an avenue to search for climate-smart plants to sustain crop and pasture productivity in the context of global climate change.
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    Electronic ISSN: 1545-2123
    Topics: Biology
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  • 3
    Publication Date: 2019-04-29
    Description: Ecological specialization in plants occurs primarily through local adaptation to different environments. Local adaptation is widely thought to result in costly fitness trade-offs that result in maladaptation to alternative environments. However, recent studies suggest that such trade-offs are not universal. Further, there is currently a limited understanding of the molecular mechanisms responsible for fitness trade-offs associated with adaptation. Here, we review the literature on stress responses in plants to identify potential mechanisms underlying local adaptation and ecological specialization. We focus on drought, high and low temperature, flooding, herbivore, and pathogen stresses. We then synthesize our findings with recent advances in the local adaptation and plant molecular biology literature. In the process, we identify mechanisms that could cause fitness trade-offs and outline scenarios where trade-offs are not a necessary consequence of adaptation. Future studies should aim to explicitly integrate molecular mechanisms into studies of local adaptation.
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  • 4
    Publication Date: 2019-04-29
    Description: In order to optimally establish their root systems, plants are endowed with several mechanisms to use at distinct steps during their development. In this review, we zoom in on the major processes involved in root development and detail important new insights that have been generated in recent studies, mainly using the Arabidopsis root as a model. First, we discuss new insights in primary root development with the characterization of tissue-specific transcription factor complexes and the identification of non-cell-autonomous control mechanisms in the root apical meristem. Next, root branching is discussed by focusing on the earliest steps in the development of a new lateral root and control of its postemergence growth. Finally, we discuss the impact of phosphate, nitrogen, and water availability on root development and summarize current knowledge about the major molecular mechanisms involved.
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  • 5
    Publication Date: 2019-04-29
    Description: Plant mitochondria play a major role during respiration by producing the ATP required for metabolism and growth. ATP is produced during oxidative phosphorylation (OXPHOS), a metabolic pathway coupling electron transfer with ADP phosphorylation via the formation and release of a proton gradient across the inner mitochondrial membrane. The OXPHOS system is composed of large, multiprotein complexes coordinating metal-containing cofactors for the transfer of electrons. In this review, we summarize the current state of knowledge about assembly of the OXPHOS complexes in land plants. We present the different steps involved in the formation of functional complexes and the regulatory mechanisms controlling the assembly pathways. Because several assembly steps have been found to be ancestral in plants—compared with those described in fungal and animal models—we discuss the evolutionary dynamics that lead to the conservation of ancestral pathways in land plant mitochondria.
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  • 6
    Publication Date: 2019-04-29
    Description: This review describes the current status and future challenges of risk assessment and regulation of plants modified by modern biotechniques, namely genetic engineering and genome editing. It provides a general overview of the biosafety and regulation of genetically modified plants and details different regulatory frameworks with a focus on the European situation. The environmental risk and safety assessment of genetically modified plants is explained, and aspects of toxicological assessments are discussed, especially the controversial debate in Europe on the added scientific value of untargeted animal feeding studies. Because RNA interference (RNAi) is increasingly explored for commercial applications, the risk and safety assessment of RNAi-based genetically modified plants is also elucidated. The production, detection, and identification of genome-edited plants are described. Recent applications of modern biotechniques, namely synthetic biology and gene drives, are discussed, and a short outlook on the future follows.
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  • 7
    Publication Date: 2019-04-29
    Description: Plant cells divide their cytoplasmic content by forming a new membrane compartment, the cell plate, via a rerouting of the secretory pathway toward the division plane aided by a dynamic cytoskeletal apparatus known as the phragmoplast. The phragmoplast expands centrifugally and directs the cell plate to the preselected division site at the plasma membrane to fuse with the parental wall. The division site is transiently decorated by the cytoskeletal preprophase band in preprophase and prophase, whereas a number of proteins discovered over the last decade reside continuously at the division site and provide a lasting spatial reference for phragmoplast guidance. Recent studies of membrane fusion at the cell plate have revealed the contribution of functionally conserved eukaryotic proteins to distinct stages of cell plate biogenesis and emphasize the coupling of cell plate formation with phragmoplast expansion. Together with novel findings concerning preprophase band function and the setup of the division site, cytokinesis and its spatial control remain an open-ended field with outstanding and challenging questions to resolve.
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  • 8
    Publication Date: 2019-04-29
    Description: During the past decade, a flurry of research focusing on the role of peptides as short- and long-distance signaling molecules in plant cell communication has been undertaken. Here, we focus on peptides derived from nonfunctional precursors, and we address several key questions regarding peptide signaling. We provide an overview of the regulatory steps involved in producing a biologically active peptide ligand that can bind its corresponding receptor(s) and discuss how this binding and subsequent activation lead to specific cellular outputs. We discuss different experimental approaches that can be used to match peptide ligands with their receptors. Lastly, we explore how peptides evolved from basic signaling units regulating essential processes in plants to more complex signaling systems as new adaptive traits developed and how nonplant organisms exploit this signaling machinery by producing peptide mimics.
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  • 9
    Publication Date: 2019-04-29
    Description: Leaf senescence is an important developmental process involving orderly disassembly of macromolecules for relocating nutrients from leaves to other organs and is critical for plants’ fitness. Leaf senescence is the response of an intricate integration of various environmental signals and leaf age information and involves a complex and highly regulated process with the coordinated actions of multiple pathways. Impressive progress has been made in understanding how senescence signals are perceived and processed, how the orderly degeneration process is regulated, how the senescence program interacts with environmental signals, and how senescence regulatory genes contribute to plant productivity and fitness. Employment of systems approaches using omics-based technologies and characterization of key regulators have been fruitful in providing newly emerging regulatory mechanisms. This review mainly discusses recent advances in systems understanding of leaf senescence from a molecular network dynamics perspective. Genetic strategies for improving the productivity and quality of crops are also described.
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  • 10
    Publication Date: 2019-08-18
    Description: Dear readers: We are sad to report that, soon after submitting her draft manuscript for this prefatory chapter, Nancy Grace Roman passed away on December 25, 2018. This final version of her memoir has been lightly edited but remains very true to the original. However, an Abstract was missing. Rather than trying to synthesize one in Nancy Grace's inimitable style, we take this opportunity to comment briefly on her life and its significance. Nancy Grace Roman was born in 1925 and came of age scientifically in the United States during the 1940s and 1950s. Together with the equally fascinating prefatory by Vera Rubin ( ARAA, Vol. 49), which we also recommend to you, these two memoirs give us intimate insight into the obstacles faced by women astronomers trying to rise in the field during those years. Roman's memoir is bitingly candid, recounting numerous snubs by teachers, insultingly small salaries, and attempts by her thesis advisor to simultaneously exploit her scientific findings and smother her role in them. Discouragement at every turn from doing forefront research is what drove Roman into government service, where she found a niche and blossomed as one of the visionary founders of the US civilian space program. We do not know what impact Roman might have had as a researcher with access to the world's largest telescopes, but we do know that her influence as an enabler of other people's science was vast. Her sobriquet as the “Mother of Hubble,” bestowed by admirer Ed Weiler, is well deserved. Nancy Grace granted an audio interview to Joss Bland-Hawthorn on August 4, 2018, just a few months before her passing. It captures her persona more vividly than mere words on paper, and we recommend the online recording to you at https://www.annualreviews.org/r/nancy-grace-roman-interview .
    Print ISSN: 0066-4146
    Electronic ISSN: 1545-4282
    Topics: Physics
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  • 11
    Publication Date: 2019-08-18
    Print ISSN: 0066-4146
    Electronic ISSN: 1545-4282
    Topics: Physics
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  • 12
    Publication Date: 2019-08-18
    Description: The recent advancements in far-infrared (far-IR) astronomy brought about by the Herschel, SOFIA, and ALMA observatories have led to technological advancements in millimeterwave and submillimeterwave laboratory spectroscopy that is used to support molecular observations. This review gives an overview of rotational spectroscopy and its relationship with observational astronomy, as well as an overview of laboratory spectroscopic techniques focusing on both historical approaches and new advancements. Additional topics discussed include production and detection techniques for unstable molecular species of astrochemical interest, data analysis approaches that address spectral complexity and line confusion, and the current state of and limitations to spectral line databases. Potential areas for new developments in this field are also reviewed. To advance the field, the following challenges must be addressed: ▪ Data acquisition speed, spectral sensitivity, and analysis approaches for complex mixtures and broadband spectra are the greatest limitations—and hold the greatest promise for advancement—in this field of research. ▪ Full science return from far-IR observatories cannot be realized until laboratory spectroscopy catches up with the data rate for observations. ▪ New techniques building on those used in the microwave and IR regimes are required to fill the terahertz gap.
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    Topics: Physics
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  • 13
    Publication Date: 2019-10-21
    Description: This article suggests that although there is not much of an explicitly defined anthropology of populism, anthropologists have nevertheless been working for many years on the things we talk about when we talk about populism. Anthropologists should thus be exceptionally well situated to divert the debate on populism in creative ways. In particular, I argue that the term populism registers an intensified insistence of collective forces that are no longer adequately organized by formerly hegemonic social forms: a mattering-forth of the collective flesh. The article also shows why populism is such an awkward topic for anthropologists. In part, this discomfort has to do with a tension between anthropologists’ effectively populist commitments to the common sense of common people at a time when that common sense can often look ugly. In part, it has to do with how the populist challenge to liberalism both aligns populist politics with anthropological critiques of liberal norms and puts pressure on anthropology's continued dependence on liberal categories for its own relevance to broader public debates.
    Print ISSN: 0084-6570
    Electronic ISSN: 1545-4290
    Topics: Biology , Ethnic Sciences
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  • 14
    Publication Date: 2019-10-21
    Description: WEIRD populations, or those categorized as Western, educated, industrialized, rich, and democratic, are sampled in the majority of quantitative human subjects research. Although this oversampling is criticized in some corners of social science research, it is not always clear what we are critiquing. In this article, we make three interventions into the WEIRD concept and its common usage. First, we seek to better operationalize the terms within WEIRD to avoid erasing people with varying identities who also live within WEIRD contexts. Second, we name whiteness as the factor that most strongly unites WEIRD research and researchers yet typically goes unacknowledged. We show how reflexivity is a tool that can help social scientists better understand the effects of whiteness within the scientific enterprise. Third, we look at the positionality of biological anthropology, as not cultural anthropology and not psychology, and how that offers both promise and pitfalls to the study of human variation. We offer other perspectives on what constitutes worthy and rigorous biological anthropology research that does not always prioritize replicability and statistical power, but rather emphasizes the full spectrum of the human experience. From here, we offer several ways forward to produce more inclusive human subjects research, particularly around existing methodologies such as grounded theory, Indigenous methodologies, and participatory action research, and call on biological anthropology to contribute to our understanding of whiteness.
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  • 15
    Publication Date: 2019-10-21
    Description: The anthropology of water is a self-declared relational field that attempts to transcend nature/culture distinctions by attending to the fact that the social and ecological aspects of water are separated only by convention. Despite its recent coming of age, the anthropology of water is incredibly expansive. It attends to molecular, embodied, ecosystemic, and planetary issues. I provide an overview of that breadth in four thematic clusters: (in)sufficiency, bodies and beings, knowledge, and ownership. These clusters highlight issues of materiality, ontological politics, and political economy. They are the grounds on which questions of water justice are elucidated. Furthermore, I show how water is always more than itself; its force and material presence constantly frame people's efforts to address the fundamental question of what it means to live life collectively in a world that is always more than human. I close with two directions for research: the denaturalization of water's materiality and the diversification of the moral undertones of our analytic vocabularies.
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  • 16
    Publication Date: 2019-10-21
    Description: In the immediate aftermath of the Cold War, Munn (1992) argued that anthropology had neglected the future as a temporal focus. This concern continues to be echoed by anthropologists, even as a review of post–Cold War anthropology reveals that the future has become a recurrent, dominant temporality in the field. Reviewing texts from the past quarter-century that provide a diagnostic at the intersection of the anthropology of futurity and the future of anthropology, we argue that the urgency for an anthropology of the future—and concern over its neglect—presumes some continuity prior to the challenges of an uncertain “now” under constant transformation and, simultaneously, a desire for a common and open future world. Deriving this insight from the work of Black and Indigenous scholars, we suggest that an anthropology attuned to futures is most fruitful when it foregrounds decolonizing perspectives on commonality, continuity, and openness and problematizes them as the implicit grounds of anthropological futurity.
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  • 17
    Publication Date: 2019-10-21
    Description: The senses are made, not given. Multisensory anthropology focuses on the variable boundaries, differential elaboration, and many different ways of combining the senses across (and within) cultures. Its methodology is grounded in “participant sensation,” or sensing—and making sense—along with others, also known as sensory ethnography. This review article traces the sensualization of anthropological theory and practice since the early 1990s, showing how the concept of sensory mediation has steadily supplanted the prior concern with representation. It concludes with a discussion of how the senses are engaged in filmmaking, multispecies ethnography, and material culture studies as well as in achieving social justice.
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  • 18
    Publication Date: 2019-10-21
    Description: Armed conflict regularly presents extremely adverse circumstances not only for combatants, but also for civilians. In fact, estimates from various wars over the past 70 years suggest that noncombatants comprise the majority of casualties. For survivors, war's effects are often embodied, leaving long-term effects on health and biology. Some of these effects, such as injuries and psychological trauma, are well known. Yet other effects may be subtle and may be elucidated by a developmental biological perspective. In early life, when growth rates are highest, conditions of war may have their greatest impact. Depending on local circumstances, a developing embryo, infant, or child growing in a place embroiled in armed conflict is likely to face—directly or indirectly—various stressors, including malnutrition, infectious disease, and/or psychological stress. Thus, the conditions of war and forced displacement may become embodied, getting under the skin for fundamental biological reasons.
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  • 19
    Publication Date: 2019-10-21
    Description: From the “verbal deprivation” and “restricted codes” of the 1960s to contemporary “language gap” discourses, deficit models of children's language have been posited to explain social ills ranging from school failure to intergenerational poverty. However, researchers from a range of disciplines have problematized such models on the basis of the power of language to reflect, articulate, produce, and reproduce structural inequality. This review considers how the discursive construction of language, poverty, and child development contributes to deficit-based research agendas and the resulting interventions aimed at remediating language use in homes and schools. We suggest that an anthropolitical language socialization approach deconstructs ideologies of linguistic (in)competence and more accurately traces how children across cultures and social contexts develop communicative resources, cultural knowledge, and social practices in the face of political and economic adversity; it also helps articulate alternative ways of respecting and building on difference.
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  • 20
    Publication Date: 2019-10-21
    Description: This article reviews the main trends in the anthropological scholarship of Islam in Europe by examining this body of work through the lens of what I call a double epistemological impasse. The first impasse refers to the historical marking of Islam as Europe's Other, and the second one concerns anthropology's discomfort with the epistemological claim making of monotheistic religious traditions. The literature is organized into three key figures (the Muslim as migrant, as Islamist, and as ethical subject), and through these figures, this article attempts to unearth how this double impasse has affected and informed anthropological scholarship on Islam in Europe.
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  • 21
    Publication Date: 2019-10-21
    Description: What constitutes “human reproduction” is under negotiation as its biology, social nature, and cultural valences are increasingly perceived as bound up in environmental issues. This review maps the growing overlap between formerly rather separate domains of reproductive politics and environmental politics, examining three interrelated areas. The first is the emergence of an intersectional environmental reproductive justice framework in activism and environmental health science. The second is the biomedical delineation of the environment of reproduction and development as an object of growing research and intervention, as well as the marking off of early-life environments as an “exposed biology” consequential to the entire life span. Third is researchers’ critical engagement with the reproductive subject of environmental politics and the lived experience of reproduction in environmentally dystopic times. Efforts to rethink the intersections of reproductive and environmental politics are found throughout these three areas.
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  • 22
    Publication Date: 2019-10-21
    Description: An enduring debate in the field of Arctic archaeology has been the extent to which climate change impacted cultural developments in the past. Long-term culture change across the circumpolar Arctic was often highly dynamic, with episodes of rapid migration, regional abandonment, and—in some cases—the disappearance or wholesale replacement of entire cultural traditions. By the 1960s, researchers were exploring the possibility that warming episodes had positive effects on cold-adapted premodern peoples in the Arctic by ( a) reducing the extent of sea ice, ( b) expanding the size and range of marine mammal populations, and ( c) opening new waterways and hunting areas for marine-adapted human groups. Although monocausal climatic arguments for change are now regarded as overly simplistic, the growing threat of contemporary Arctic warming to Indigenous livelihoods has given wider relevance to research into long-term culture–climate interactions. With their capacity to examine deeper cultural responses to climate change, archaeologists are in a unique position to generate human-scale climate adaptation insights that may inform future planning and mitigation efforts. The exceptionally well-preserved cultural and paleo-ecological sequences of the Arctic make it one of the best-suited regions on Earth to address such problems. Ironically, while archaeologists employ an exciting and highly promising new generation of methods and approaches to examine long-term fragility and resilience in Arctic social-ecological systems, many of these frozen paleo-societal archives are fast disappearing due to anthropogenic warming.
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  • 23
    Publication Date: 2019-10-21
    Description: Citizenship has become a major topic in anthropology and the study of language (including sociolinguistics) since the early 1990s, with scholars in these fields especially examining the status and political claims of immigrants, refugees, indigenous groups, and other subaltern populations. This article argues that models of communication lie at the heart of debates about citizenship and explores two fundamentally communicative processes: first, the mutual recognition of citizens as citizens, and second, the interpellation by state apparatuses of citizens. It first discusses the emergence of the question of citizenship within anthropology and the study of language. It then considers the tension that arises as any recognition of difference confronts the normative model of citizenship already institutionalized in the state apparatus. Finally, this article examines the interlacing of these scholarly trajectories in one of the premier sites where citizens communicate as citizens: the public sphere.
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  • 24
    Publication Date: 2019-02-15
    Description: Conservation genomics aims to preserve the viability of populations and the biodiversity of living organisms. Invertebrate organisms represent 95% of animal biodiversity; however, few genomic resources currently exist for the group. The subset of marine invertebrates includes the most ancient metazoan lineages and possesses codes for unique gene products and possible keys to adaptation. The benefits of supporting invertebrate conservation genomics research (e.g., likely discovery of novel genes, protein regulatory mechanisms, genomic innovations, and transposable elements) outweigh the various hurdles (rare, small, or polymorphic starting materials). Here we review best conservation genomics practices in the laboratory and in silico when applied to marine invertebrates and also showcase unique features in several case studies of acroporid corals, crown-of-thorns starfish, apple snails, and abalone. Marine conservation genomics should also address how diversity can lead to unique marine innovations, the impact of deleterious variation, and how genomic monitoring and profiling could positively affect broader conservation goals (e.g., value of baseline data for in situ/ex situ genomic stocks).
    Print ISSN: 2165-8102
    Electronic ISSN: 2165-8110
    Topics: Biology
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  • 25
    Publication Date: 2019-02-15
    Description: The demand for food will increase to an unprecedented level over the next 30 years owing to human population expansion, thus necessitating an evolution that improves the efficiency of livestock production. Genetic gain to improve production traits of domestic animal populations is most effectively achieved via selective use of gametes from animals deemed to be elite, and this principle has been the basis of selective breeding strategies employed by humans for thousands of years. In modern-day animal agriculture, artificial insemination (AI) has been the staple of selective breeding programs, but it has inherent limitations for applications in beef cattle and pig production systems. In this review, we discuss the potential and current state of development for a concept termed Surrogate Sires as a next-generation breeding tool in livestock production. The scheme capitalizes on the capacity of spermatogonial stem cells to regenerate sperm production after isolation from donor testicular tissue and transfer into the testes of a recipient male that lacks endogenous germline, thereby allowing the surrogate male to produce offspring with the donor haplotype via natural mating. This concept provides an effective selective breeding tool to achieve genetic gain that is conducive for livestock production systems in which AI is difficult to implement.
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  • 26
    Publication Date: 2019-06-12
    Description: Electrochemical measurements of neurotransmitters provide insight into the dynamics of neurotransmission. In this review, we describe the development of electrochemical measurements of neurotransmitters and how they started with extrasynaptic measurements but now are pushing toward synaptic measurements. Traditionally, biosensors or fast-scan cyclic voltammetry have monitored extrasynaptic levels of neurotransmitters, such as dopamine, serotonin, adenosine, glutamate, and acetylcholine. Amperometry and electrochemical cytometry techniques have revealed mechanisms of exocytosis, suggesting partial release. Advances in nanoelectrodes now allow spatially resolved, electrochemical measurements in a synapse, which is only 20–100 nm wide. Synaptic measurements of dopamine and acetylcholine have been made. In this article, electrochemical measurements are also compared to optical imaging and mass spectrometry measurements, and while these other techniques provide enhanced spatial or chemical information, electrochemistry is best at monitoring real-time neurotransmission. Future challenges include combining electrochemistry with these other techniques in order to facilitate multisite and multianalyte monitoring.
    Print ISSN: 1936-1327
    Electronic ISSN: 1936-1335
    Topics: Chemistry and Pharmacology
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  • 27
    Publication Date: 2019-06-12
    Description: Sweat is a largely unexplored biofluid that contains many important biomarkers ranging from electrolytes and metabolites to proteins, cytokines, antigens, and exogenous drugs. The eccrine and apocrine glands produce and excrete sweat through microscale pores on the epidermal surface, offering a noninvasive means for capturing and probing biomarkers that reflect hydration state, fatigue, nutrition, and physiological changes. Recent advances in skin-interfaced wearable sensors capable of real-time in situ sweat collection and analytics provide capabilities for continuous biochemical monitoring in an ambulatory mode of operation. This review presents a broad overview of sweat-based biochemical sensor technologies with an emphasis on enabling materials, designs, and target analytes of interest. The article concludes with a summary of challenges and opportunities for researchers and clinicians in this swiftly growing field.
    Print ISSN: 1936-1327
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    Topics: Chemistry and Pharmacology
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  • 28
    Publication Date: 2019-06-12
    Description: Although fluorescent reporters and biosensors have become indispensable tools in biological and biomedical fields, fluorescence measurements require external excitation light, thereby limiting their use in thick tissues and live animals. Bioluminescent reporters and biosensors may potentially overcome this hurdle because they use enzyme-catalyzed exothermic biochemical reactions to generate excited-state emitters. This review first introduces the development of bioluminescent reporters, and next, their applications in sensing biological changes in vitro and in vivo as biosensors. Lastly, we discuss chemiluminescent sensors that produce photons in the absence of luciferases. This review aims to explore fundamentals and experimental insights and to emphasize the yet-to-be-reached potential of next-generation luminescent reporters and biosensors.
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    Topics: Chemistry and Pharmacology
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  • 29
    Publication Date: 2019-06-12
    Description: There is an increasing appreciation that every cell, even of the same type, is different. This complexity, when additionally combined with the variety of different cell types in tissue, is driving the need for spatially resolved omics at the single-cell scale. Rapid advances are being made in genomics and transcriptomics, but progress in metabolomics lags. This is partly because amplification and tagging strategies are not suited to dynamically created metabolite molecules. Mass spectrometry imaging has excellent potential for metabolic imaging. This review summarizes the recent advances in two of these techniques: matrix-assisted laser desorption ionization (MALDI) and secondary ion mass spectrometry (SIMS) and their convergence in subcellular spatial resolution and molecular information. The barriers that have held back progress such as lack of sensitivity and the breakthroughs that have been made including laser-postionization are highlighted as well as the future challenges and opportunities for metabolic imaging at the single-cell scale.
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    Topics: Chemistry and Pharmacology
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  • 30
    Publication Date: 2019-06-12
    Description: Experimental techniques to monitor and visualize the behaviors of single nanoparticles have not only revealed the significant spatial and temporal heterogeneity of those individuals, which are hidden in ensemble methods, but more importantly, they have also enabled researchers to elucidate the origin of such heterogeneity. In pursuing the intrinsic structure-function relations of single nanoparticles, the recently developed stochastic collision approach demonstrated some early promise. However, it was later realized that the appropriate sizing of a single nanoparticle by an electrochemical method could be far more challenging than initially expected owing to the dynamic motion of nanoparticles in electrolytes and complex charge-transfer characteristics at electrode surfaces. This clearly indicates a strong necessity to integrate single nanoparticle electrochemistry with high-resolution optical microscopy. Hence, this review aims to give a timely update of the latest progress for both electrochemically sensing and seeing single nanoparticles. A major focus is on collision-based measurements, where nanoparticles or single entities in solution impact on a collector electrode and the electrochemical response is recorded. These measurements are further enhanced with optical measurements in parallel. For completeness, advances in other related methods for single nanoparticle electrochemistry are also included.
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  • 31
    Publication Date: 2019-06-12
    Description: Surface plasmon resonance microscopy and imaging are optical methods that enable observation and quantification of interactions of nano- and microscale objects near a metal surface in a temporally and spatially resolved manner. This review describes the principles of surface plasmon resonance microscopy and imaging and discusses recent advances in these methods, in particular, in optical platforms and functional coatings. In addition, the biological applications of these methods are reviewed. These include the detection of a broad variety of analytes (nucleic acids, proteins, bacteria), the investigation of biological systems (bacteria and cells), and biomolecular interactions (drug–receptor, protein–protein, protein–DNA, protein–cell).
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  • 32
    Publication Date: 2019-02-15
    Description: Of all the big cats, or perhaps of all the endangered wildlife, the tiger may be both the most charismatic and most well-recognized flagship species in the world. The rapidly changing field of molecular genetics, particularly advances in genome sequencing technologies, has provided new tools to reconstruct what characterizes a tiger. Here we review how applications of molecular genomic tools have been used to depict the tiger's ancestral roots, phylogenetic hierarchy, demographic history, morphological diversity, and genetic patterns of diversification on both temporal and geographical scales. Tiger conservation, stabilization, and management are important areas that benefit from use of these genome resources for developing survival strategies for this charismatic megafauna both in situ and ex situ.
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  • 33
    Publication Date: 2019-06-12
    Description: Analysis of nanoscale biological particles and organelles (BPOs) at the single-particle level is fundamental to the in-depth study of biosciences. Flow cytometry is a versatile technique that has been well-established for the analysis of eukaryotic cells, yet conventional flow cytometry can hardly meet the sensitivity requirement for nanoscale BPOs. Recent advances in high-sensitivity flow cytometry have made it possible to conduct precise, sensitive, and specific analyses of nanoscale BPOs, with exceptional benefits for bacteria, mitochondria, viruses, and extracellular vesicles (EVs). In this article, we discuss the significance, challenges, and efforts toward sensitivity enhancement, followed by the introduction of flow cytometric analysis of nanoscale BPOs. With the development of the nano-flow cytometer that can detect single viruses and EVs as small as 27 nm and 40 nm, respectively, more exciting applications in nanoscale BPO analysis can be envisioned.
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  • 34
    Publication Date: 2019-06-12
    Description: Lasers with pulse lengths from nanoseconds to femtoseconds and wavelengths from the mid-infrared to extreme ultraviolet (UV) have been used for desorption or ablation in mass spectrometry. Such laser sampling can often benefit from the addition of a second laser for postionization of neutrals. The advantages offered by laser postionization include the ability to forego matrix application, high lateral resolution, decoupling of ionization from desorption, improved analysis of electrically insulating samples, and potential for high sensitivity and depth profiling while minimizing differential detection. A description of postionization by vacuum UV radiation is followed by a consideration of multiphoton, short pulse, and other postionization strategies. The impacts of laser pulse length and wavelength are considered for laser desorption or laser ablation at low pressures. Atomic and molecular analysis via direct laser desorption/ionization using near-infrared ultrashort pulses is described. Finally, the postionization of clusters, the role of gaseous collisions, sampling at ambient pressure, atmospheric pressure photoionization, and the addition of UV postionization to MALDI are considered.
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  • 35
    Publication Date: 2019-06-12
    Description: Atmospheric aerosol, particulate matter suspended in the air we breathe, exerts a strong impact on our health and the environment. Controlling the amount of particulate matter in air is difficult, as there are many ways particles can form by both natural and anthropogenic processes. We gain insight into the sources of particulate matter through chemical composition measurements. A substantial portion of atmospheric aerosol is organic, and this organic matter is exceedingly complex on a molecular scale, encompassing hundreds to thousands of individual compounds that distribute between the gas and particle phases. Because of this complexity, no single analytical technique is sufficient. However, mass spectrometry plays a crucial role owing to its combination of high sensitivity and molecular specificity. This review surveys the various ways mass spectrometry is used to characterize atmospheric organic aerosol at a molecular level, tracing these methods from inception to current practice, with emphasis on current and emerging areas of research. Both offline and online approaches are covered, and molecular measurements with them are discussed in the context of identifying sources and elucidating the underlying chemical mechanisms of particle formation. There is an ongoing need to improve existing techniques and develop new ones if we are to further advance our knowledge of how to mitigate the unwanted health and environmental impacts of particles.
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  • 36
    Publication Date: 2019-06-12
    Description: Extended X-ray absorption fine structure (EXAFS) spectroscopy is a premiere method for analysis of the structure and structural transformation of nanoparticles. Extraction of analytical information about the three-dimensional structure and dynamics of metal–metal bonds from EXAFS spectra requires special care due to their markedly non-bulk-like character. In recent decades, significant progress has been made in the first-principles modeling of structure and properties of nanoparticles. In this review, we summarize new approaches for EXAFS data analysis that incorporate particle structure modeling into the process of structural refinement.
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  • 37
    Publication Date: 2019-06-12
    Description: The helium ion microscope (HIM) has emerged as an instrument of choice for patterning, imaging and, more recently, analytics at the nanoscale. Here, we review secondary electron imaging on the HIM and the various methodologies and hardware components that have been developed to confer analytical capabilities to the HIM. Secondary electron–based imaging can be performed at resolutions down to 0.5 nm with high contrast, with high depth of field, and directly on insulating samples. Analytical methods include secondary electron hyperspectral imaging (SEHI), scanning transmission ion microscopy (STIM), backscattering spectrometry and, in particular, secondary ion mass spectrometry (SIMS). The SIMS system that was specifically designed for the HIM allows the detection of all elements, the differentiation between isotopes, and the detection of trace elements. It provides mass spectra, depth profiles, and 2D or 3D images with lateral resolutions down to 10 nm.
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  • 38
    Publication Date: 2019-06-12
    Description: Lithium battery technologies have revolutionized mobile energy storage, but improvements in the technology are still needed. Critical to delivering new light weight, high capacity, safe devices is an improved understanding of the dynamic processes occurring at the electrode-electrolyte interfaces. Therefore, alongside advances in materials there has been a parallel progression in advanced characterization methods. Herein, recent developments for operando spectro-electrochemical techniques centered on Raman, infrared, and sum frequency generation are described within the context of lithium-ion and non-aqueous lithium-oxygen battery research. In particular, shell-isolated nanoparticles for enhanced Raman spectroscopy (SHINERS), surface-enhanced infrared absorption spectroscopy (SEIRAS), and near-field infrared are explained and critically evaluated, and future opportunities discussed. The aim is to introduce the wider community to the developing range of methodologies and tools now available in the hope that it encourages greater usage across the sector.
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  • 39
    Publication Date: 2019-10-21
    Description: Human societies show a deep concern with how people know things and how relationships to knowledge are constructed and portrayed in talk. The term evidentiality refers to particular linguistic resources for talking about knowledge and especially to grammaticalized markers that indicate knowledge sources. Evidential marking is found in diverse languages around the world. This review discusses cross-linguistic evidential meanings and examines research on evidentials in practice, with a focus on their interpretation as stance markers and deictic elements. Evidentiality is a fascinating accomplishment in language structure, meaning, and use and can tell us about shared and disparate visions of knowledge and sociality across cultures.
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    Topics: Biology , Ethnic Sciences
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  • 40
    Publication Date: 2019-10-21
    Description: Physician anthropologists have contributed extensively to the anthropology of biomedicine, as well as to other aspects of medical anthropology. Their use of detailed clinical case narratives allows elucidation of what is at stake for individuals and communities in the course of any given illness. Biomedically informed observations of bodies illustrate the connections between microscopic harm and macrosocial arrangements, while observations of clinical spaces and medical knowledge production contribute to current debates over evidence, metrics, migration, and humanitarianism. In moving away from culturalist explanations for illness, physician anthropologists have drawn attention to the manifold workings of structural violence—and have often sacrificed the possibility of deep epistemological challenges to biomedicine. While raising a note of caution about the moral authority of physician anthropologists, I recognize that much of this scholarship has laid the intellectual groundwork for a movement toward equity that refuses to justify poor-quality health care for poor people.
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  • 41
    Publication Date: 2019-10-21
    Description: This article reviews how the analytics of governmentality have been taken up by scholars in linguistic anthropology, sociolinguistics, and applied linguistics. It explores the distinctive logics of “linguistic governmentality” understood as techniques and forms of expertise that seek to govern, guide, and shape (rather than force) linguistic conduct and subjectivity at the level of the population or the individual. Governmentality brings new perspectives to the study of language ideologies and practices informing modernist and neoliberal language planning and policies, the technologies of knowledge they generate, and the contestations that surround them. Recent work in this vein is deepening our understanding of “language”—understood as an array of verbal and nonverbal communicative practices—as a medium through which neoliberal governmentality is exercised. The article concludes by considering how a critical sociolinguistics of governmentality can address some shortcomings in the study of governmentality and advance the study of language, power, and inequality.
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  • 42
    Publication Date: 2019-10-21
    Description: This article presents an autobiographical perspective on the changing nature of Maya archaeology, focusing on the role of settlement pattern studies in illuminating the lives of commoners as well as on the traditional emphasis on the ruling elite. Advances in understanding the nature of nonelite peoples in ancient Maya society are discussed, as are the many current gaps in scholarly understandings of pre-Columbian Maya civilization, especially with regard to the diversity of ancient “commoners” and the difficulty in analyzing them as a single group.
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  • 43
    Publication Date: 2019-10-21
    Description: This article examines the question of why local food has become, for many activists and scholars, a core concept for understanding food systems and globalization and for challenging systems of injustice and inequality. I begin with the French concept of terroir, which is often translated as the “taste of place,” and examine why this term, part of France's cultural common sense, is difficult to implement in other places. I then consider efforts to use local foods to grapple with the forces of globalization and efforts to use ideas about local food to moralize capitalism and humanize food distribution systems. I examine the relationship between movements for food sovereignty and food justice with local foods. Finally, I explore the uses of local foods as part of efforts to develop, assert, and sometimes market local, regional, or national identities.
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  • 44
    Publication Date: 2019-10-21
    Description: That the meanings and value of things can be transformed through their circulation was brought to the foreground of anthropological studies more than 30 years ago with the publication of The Social Life of Things (Appadurai 1986b). The last decade, however, has seen a move away from “object biographies” in favor of frameworks that better account for objects’ complex entanglements. Recent work on object itineraries extends and challenges many elements of the biography approach and represents an intersection with critical interventions regarding materiality and agency, networks and circulation, and heritage discourses. This review evaluates the legacy of The Social Life of Things in the context of anthropological studies of the material world and suggests that thinking about itineraries rather than biographies allows us to collapse the distinctions between past and present (and future) and, thus, fully consider objects’ present entanglements as central to their story.
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  • 45
    Publication Date: 2019-10-21
    Description: This article brings together classic work in the anthropology of death, much of which focused on funerary rites, with more recent studies, some of which continue with the classic focus and some of which introduce distinct views and problematics. The anthropology of death has become a capacious field, linking to broader debates on violence, suffering, medicine, subjectivity, race, gender, faith, modernity, and secularity (among others). In much of this work, though, we find common concerns with, and recurrent considerations of, certain themes. This review focuses on two of the most important: the symbolic imaginaries of how life conquers death; and, even more centrally, the materiality of death. A range of topics are addressed, including putrescence, burial, bones, commemorations, debts, care, sovereignty, and personal loss.
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  • 46
    Publication Date: 2019-10-21
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  • 47
    Publication Date: 2019-10-21
    Description: Language endangerment by definition excludes children and childhood, as the most endangered languages are those which are no longer being used, spoken, or acquired by the youngest generations. By and large, research in this area reflects this exclusion by focusing primarily on the documentation of grammatical knowledge elicited from the oldest speakers for storage in archives (what Maliseet anthropologist Bernard Perley has termed “zombie linguistics”). However, when approached from a language socialization orientation, the seeming paradox of language endangerment in childhood dissolves. Investigations of endangered languages in childhood reveal surprisingly vibrant and complicated amalgams of linguistic practices, socializing discourses, and cultural ideologies. They underscore the need to apply mixed methods to understanding processes of language endangerment. They challenge the grammatical boundedness of languages as (transparently) discrete objects. They recognize the vitalities emergent from situations of aggressive contact. Thus, attention to children and childhood not only calls into question the privileged rhetoric of zombie linguistics but also accentuates and challenges the socially constructed dimensions of languages and linguistic boundaries.
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  • 48
    Publication Date: 2019-10-21
    Description: We focus on the anthropology of art from the mid-1980s to the present, a period of disturbance and significant transformation in the field of anthropology. The field can be understood to be responding to the destabilization of the category of “art” itself. Inaugural moments lie in the reaction to the Museum of Modern Art's 1984 exhibition “Primitivism” in 20th Century Art, the increasing crisis of representation, the influence of “postmodernism,” and the rising tide of decolonization and globalization, marked by the 1984 Te Maori exhibition at the Metropolitan Museum in New York. Changes involve boundaries being negotiated, violated, and refigured, and not simply the boundaries between the so-called “West” and “the rest” but also those of “high” and “low,” leading to a re-evaluation of public culture. In this review, we pursue the influence of changing theories of art and engagements with what had been noncanonical art in the mainstream art world, tracing multiple intersections between art and anthropology in the contemporary moment.
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  • 49
    Publication Date: 2019-10-21
    Description: This article considers the ongoing importance of studying writing practices within and beyond anthropology. The works included here concentrate on scholarship that has appeared since the productive yet divisive debates that established literacy as a plural phenomenon that is best studied ethnographically. It focuses on research that surveys the multiplicity of graphic forms, the changing notions of literacies, and the ways that literacy is implicated in and constitutive of sites of power. In addition, the cited works engage with the linguistic and semiotic ideologies that inform such literacy practices, the various aesthetic sensibilities that shape writing, and the physicality/materiality of inscriptive practices. Considering the effects of previously theorizing writing as a single, uniform phenomenon and the shift to research that characterizes inscriptive practices as multiple makes possible an argument for moving beyond multiplicity to question what writing is and can be, looking to works on “inscriptive practices” and “graphic pluralism.”
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  • 50
    Publication Date: 2019-02-15
    Description: Bacteria are ubiquitous in the bovine uterus after parturition, but 50 years ago, cows tolerated these bacteria and few animals developed uterine disease. Now, up to 40% of dairy cattle develop postpartum uterine disease. Uterine disease causes infertility by compromising the function of not only the endometrium but also the ovary. Animals defend themselves against pathogens using tolerance and resistance mechanisms. Tolerance is the ability to limit the disease severity induced by a given pathogen burden. Resistance is the ability to limit the pathogen burden and is usually the function of immunity. Endometrial cells contribute to tolerance and have roles in innate immunity and the inflammatory response to pathogens. However, failures in endometrial tolerance and the character of the inflammatory response shape postpartum uterine disease. We propose that uterine health is more dependent on the ability of the endometrium to tolerate pathogens than the ability to resist invading bacteria.
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  • 51
    Publication Date: 2019-02-15
    Description: In vertebrates, sex organs are generally specialized to perform a male or female reproductive role. Acquisition of the Müllerian duct, which gives rise to the oviduct, together with emergence of the Amh/Amhr2 system favored evolution of viviparity in jawed vertebrates. Species with high sex-specific reproductive adaptations have less potential to sex reverse, making intersex a nonfunctional condition. Teleosts, the only vertebrate group in which hermaphroditism evolved as a natural reproductive strategy, lost the Müllerian duct during evolution. They developed for gamete release complete independence from the urinary system, creating optimal anatomic and developmental preconditions for physiological sex change. The common and probably ancestral role of Amh is related to survival and proliferation of germ cells in early and adult gonads of both sexes rather than induction of Müllerian duct regression. The relationship between germ cell maintenance and sex differentiation is most evident in species in which Amh became the master male sex–determining gene.
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  • 52
    Publication Date: 2019-02-15
    Description: The 1000 Bull Genomes Project is a collection of whole-genome sequences from 2,703 individuals capturing a significant proportion of the world's cattle diversity. So far, 84 million single-nucleotide polymorphisms (SNPs) and 2.5 million small insertion deletions have been identified in the collection, a very high level of genetic diversity. The project has greatly accelerated the identification of deleterious mutations for a range of genetic diseases, as well as for embryonic lethals. The rate of identification of causal mutations for complex traits has been slower, reflecting the typically small effect size of these mutations and the fact that many are likely in as-yet-unannotated regulatory regions. Both the deleterious mutations that have been identified and the mutations associated with complex trait variation have been included in low-cost SNP array designs, and these arrays are being genotyped in tens of thousands of dairy and beef cattle, enabling management of deleterious mutations in these populations as well as genomic selection.
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  • 53
    Publication Date: 2019-02-15
    Description: Consumption of animal products such as meat, milk, and eggs in first-world countries has leveled off, but it is rising precipitously in developing countries. Agriculture will have to increase its output to meet demand, opening the door to increased automation and technological innovation; intensified, sustainable farming; and precision livestock farming (PLF) applications. Early indicators of medical problems, which use sensors to alert cattle farmers early concerning individual animals that need special care, are proliferating. Wearable technologies dominate the market. In less-value-per-animal systems like sheep, goat, pig, poultry, and fish, one sensor, like a camera or robot per herd/flock/school, rather than one sensor per animal, will become common. PLF sensors generate huge amounts of data, and many actors benefit from PLF data. No standards currently exist for sharing sensor-generated data, limiting the use of commercial sensors. Technologies providing accurate data can enhance a well-managed farm. Development of methods to turn the data into actionable solutions is critical.
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  • 54
    Publication Date: 2019-02-15
    Description: Feed protein supplements are one of the most expensive and limiting feed ingredients. This review offers a comprehensive analysis of how the expected expansion of animal production, driven by the rising world population and living standards for more animal-sourced foods, is creating a global shortage of feed protein supply. Because ruminants, chickens, and pigs contribute to 96% of the global supply of animal protein and aquaculture is growing fast, means of meeting the feed protein requirements of these species are elaborated. Geographic variation and interdependence among China, Europe, and North America in the demand and supply of feed protein are compared. The potential and current state of exploration into alternative feed proteins, including microalgae, insects, single-cell proteins, and coproducts, are highlighted. Strategic innovations are proposed to upgrade feed protein processing and assessment, improve protein digestion by exogenous enzymes, and genetically select feed-efficient livestock breeds. An overall successful and sustainable solution in meeting global feed protein demands will lead to a substantial net gain of human-edible animal protein with a minimal environmental footprint.
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  • 55
    Publication Date: 2019-02-15
    Description: Affordable, high-throughput DNA sequencing has accelerated the pace of genome assembly over the past decade. Genome assemblies from high-throughput, short-read sequencing, however, are often not as contiguous as the first generation of genome assemblies. Whereas early genome assembly projects were often aided by clone maps or other mapping data, many current assembly projects forego these scaffolding data and only assemble genomes into smaller segments. Recently, new technologies have been invented that allow chromosome-scale assembly at a lower cost and faster speed than traditional methods. Here, we give an overview of the problem of chromosome-scale assembly and traditional methods for tackling this problem. We then review new technologies for chromosome-scale assembly and recent genome projects that used these technologies to create highly contiguous genome assemblies at low cost.
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  • 56
    Publication Date: 2019-02-15
    Description: Dogs are second only to humans in medical surveillance and preventative health care, leading to a recent perception of increased cancer incidence. Scientific priorities in veterinary oncology have thus shifted, with a demand for cancer genetic screens, better diagnostics, and more effective therapies. Most dog breeds came into existence within the last 300 years, and many are derived from small numbers of founders. Each has undergone strong artificial selection, in which dog fanciers selected for many traits, including body size, fur type, color, skull shape, and behavior, to create novel breeds. The adoption of the breed barrier rule—no dog may become a registered member of a breed unless both its dam and its sire are registered members—ensures a relatively closed genetic pool within each breed. As a result, there is strong phenotypic homogeneity within breeds but extraordinary phenotypic variation between breeds. One consequence of this is the high level of breed-associated genetic disease. We and others have taken advantage of this to identify genes for a large number of canine maladies for which mouse models do not exist, particularly with regard to cancer.
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  • 57
    Publication Date: 2019-02-15
    Description: Functional annotation of genomes is a prerequisite for contemporary basic and applied genomic research, yet farmed animal genomics is deficient in such annotation. To address this, the FAANG (Functional Annotation of Animal Genomes) Consortium is producing genome-wide data sets on RNA expression, DNA methylation, and chromatin modification, as well as chromatin accessibility and interactions. In addition to informing our understanding of genome function, including comparative approaches to elucidate constrained sequence or epigenetic elements, these annotation maps will improve the precision and sensitivity of genomic selection for animal improvement. A scientific community–driven effort has already created a coordinated data collection and analysis enterprise crucial for the success of this global effort. Although it is early in this continuing process, functional data have already been produced and application to genetic improvement reported. The functional annotation delivered by the FAANG initiative will add value and utility to the greatly improved genome sequences being established for domesticated animal species.
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  • 58
    Publication Date: 2019-02-15
    Description: Rapidly improving sequencing technology coupled with computational developments in sequence assembly are making reference-quality genome assembly economical. Hundreds of vertebrate genome assemblies are now publicly available, and projects are being proposed to sequence thousands of additional species in the next few years. Such dense sampling of the tree of life should give an unprecedented new understanding of evolution and allow a detailed determination of the events that led to the wealth of biodiversity around us. To gain this knowledge, these new genomes must be compared through genome alignment (at the sequence level) and comparative annotation (at the gene level). However, different alignment and annotation methods have different characteristics; before starting a comparative genomics analysis, it is important to understand the nature of, and biases and limitations inherent in, the chosen methods. This review is intended to act as a technical but high-level overview of the field that should provide this understanding. We briefly survey the state of the genome alignment and comparative annotation fields and potential future directions for these fields in a new, large-scale era of comparative genomics.
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  • 59
    Publication Date: 2019-02-15
    Description: The functional unit in skeletal muscle is the multinucleated myofiber, which is composed of parallel arrays of microfibrils. The myofiber and sarco-mere structure of skeletal muscle are established during embryogenesis, when mononuclear myoblast cells fuse to form multinucleated myotubes and develop into muscle fibers. With the myoblasts permanently unable to enter a proliferative state again after they fuse to form the multinucleated myotube, postnatal myofiber growth, muscle homeostasis, and myofiber regeneration are dependent on a myogenic stem cell, the satellite cell. Because the satellite cell is a partially differentiated stem cell controlling the state of skeletal muscle structure throughout the life of the bird, it can impact muscle development and structure, growth, and regeneration and, subsequently, meat quality. When myofibers are damaged, muscle repair is dependent on the satellite cells. Regenerated myofibers after the repair process should be similar to the original muscle fiber. Despite significant improvements in meat-type birds, degenerative myopathies have arisen. In many of these degenerative breast muscle myopathies, like Wooden Breast, satellite cell–mediated regeneration of muscle is suppressed. Thus, the biological function of avian myogenic satellite cells and their influence on cellular mechanisms affecting breast muscle development and growth, function during degenerative myopathies, and meat quality are discussed.
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  • 60
    Publication Date: 2019-02-15
    Description: Anthropogenic environmental change has led to unprecedented rates of species extinction, presenting a major threat to global biodiversity. Among vertebrates, amphibians have been most severely impacted, with an estimated 41% of species now threatened with extinction. In response to this biodiversity crisis, a moral and ethical obligation exists to implement proactive interventionist conservation actions to assist species recovery and decelerate declines. Conservation breeding programs have been successfully established for several threatened amphibian species globally, aiming to prevent species’ extinction by maintaining genetically representative assurance colonies ex situ while providing individuals for population augmentation, translocation, and reestablishment in situ. Reproductive technologies have enormous potential to enhance the propagation and genetic management of threatened species. In this review, we discuss the role of reproductive technologies in amphibian conservation breeding programs and summarize technological advancements in amphibian hormone therapies, gamete storage, and artificial fertilization.
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  • 61
    Publication Date: 2019-02-15
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  • 62
    Publication Date: 2019-02-15
    Description: Skeletal muscle growth during the early postnatal period is rapid in the pig and dependent on the capacity of muscle to respond to anabolic and catabolic stimuli. Muscle mass is driven by the balance between protein synthesis and degradation. Among these processes, muscle protein synthesis in the piglet is exceptionally sensitive to the feeding-induced postprandial changes in insulin and amino acids, whereas muscle protein degradation is affected only during specific catabolic states. The developmental decline in the response of muscle to feeding is associated with changes in the signaling pathways located upstream and downstream of the mechanistic target of rapamycin protein complex. Additionally, muscle growth is supported by an accretion of nuclei derived from satellite cells. Activated satellite cells undergo proliferation, differentiation, and fusion with adjacent growing muscle fibers. Enhancing early muscle growth through modifying protein synthesis, degradation, and satellite cell activity is key to maximizing performance, productivity, and lifelong pig health.
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  • 63
    Publication Date: 2019-02-15
    Description: All mammalian uteri contain glands that synthesize or transport and secrete substances into the uterine lumen. Uterine gland development, or adenogenesis, is uniquely a postnatal event in sheep and pigs and involves differentiation of glandular epithelium from luminal epithelium, followed by invagination and coiling morphogenesis throughout the stroma. Intrinsic transcription factors and extrinsic factors from the ovary and pituitary as well as the mammary gland (lactocrine) regulate uterine adenogenesis. Recurrent pregnancy loss is observed in the ovine uterine gland knockout sheep, providing unequivocal evidence that glands and their products are essential for fertility. Uterine gland hyperplasia and hypertrophy during pregnancy are controlled by sequential actions of hormones from the ovary and/or pituitary as well as the placenta. Gland-derived histotroph is transported by placental areolae for fetal growth. Increased knowledge of uterine gland biology is expected to improve pregnancy outcomes, as well as the health and productivity of mothers and their offspring.
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  • 64
    Publication Date: 2019-02-15
    Description: Organisms use changes in photoperiod for seasonal reproduction to maximize the survival of their offspring. Birds have sophisticated seasonal mechanisms and are therefore excellent models for studying these phenomena. Birds perceive light via deep-brain photoreceptors and long day–induced thyroid-stimulating hormone (TSH, thyrotropin) in the pars tuberalis of the pituitary gland (PT), which cause local thyroid hormone activation within the mediobasal hypothalamus. The local bioactive thyroid hormone controls seasonal gonadotropin-releasing hormone secretion and subsequent gonadotropin secretion. In mammals, the eyes are believed to be the only photoreceptor organ, and nocturnal melatonin secretion triggers an endocrine signal that communicates information about the photoperiod to the PT to regulate TSH. In contrast, in Salmonidae fish the input pathway to the neuroendocrine output pathway appears to be localized in the saccus vasculosus. Thus, comparative analysis is an effective way to uncover the universality and diversity of fundamental traits in various organisms.
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  • 65
    Publication Date: 2019-06-12
    Description: The study of e-cigarette aerosol properties can inform public health while longer-term epidemiological investigations are ongoing. The determination of aerosol levels of known toxins, as well as of molecules with unknown inhalation toxicity profiles, affords specific information for estimating the risks of e-cigarettes and for uncovering areas that should be prioritized for further investigation.
    Print ISSN: 1936-1327
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    Topics: Chemistry and Pharmacology
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  • 66
    Publication Date: 2019-06-12
    Description: Separations of bioanalytes require robust, effective, and selective migration phenomena. However, due to the complexity of biological matrices such as body fluids or tissue, these requirements are difficult to achieve. The separations field is thus constantly evolving to develop suitable methods to separate biomarkers and fractionate biospecimens for further interrogation of biomolecular content. Advances in the field of microfabrication allow the tailored generation of micro- and nanofluidic environments. These can be exploited to induce interactions and dynamics of biological species with the corresponding geometrical features, which in turn can be capitalized for novel separation approaches. This review provides an overview of several unique separation applications demonstrated in recent years in tailored micro- and nanofluidic environments. These include electrokinetic methods such as dielectrophoresis and electrophoresis, but also rather nonintuitive ratchet separation mechanisms, continuous flow separations, and fractionations such as deterministic lateral displacement, as well as methods employing entropic forces for separation.
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  • 67
    Publication Date: 2019-06-12
    Description: Vibrational spectroscopy has contributed to the understanding of biological materials for many years. As the technology has advanced, the technique has been brought to bear on the analysis of whole organisms. Here, we discuss advanced and recently developed infrared and Raman spectroscopic instrumentation to whole-organism analysis. We highlight many of the recent contributions made in this relatively new area of spectroscopy, particularly addressing organisms associated with disease with emphasis on diagnosis and treatment. The application of vibrational spectroscopic techniques to entire organisms is still in its infancy, but new developments in imaging and chemometric processing will likely expand in the field in the near future.
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  • 68
    Publication Date: 2019-06-12
    Description: Thousands of transcripts and proteins confer function and discriminate cell types in the body. Using high-parameter technologies, we can now measure many of these markers at once, and multiple platforms are now capable of analysis on a cell-by-cell basis. Three high-parameter single-cell technologies have particular potential for discovering new biomarkers, revealing disease mechanisms, and increasing our fundamental understanding of cell biology. We review these three platforms (high-parameter flow cytometry, mass cytometry, and a new class of technologies called integrated molecular cytometry platforms) in this article. We describe the underlying hardware and instrumentation, the reagents involved, and the limitations and advantages of each platform. We also highlight the emerging field of high-parameter single-cell data analysis, providing an accessible overview of the data analysis process and choice of tools.
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  • 69
    Publication Date: 2019-10-21
    Description: While the categories of adolescence and puberty are often treated as one, the existence of two distinct terms points to different kinds of maturation in humans. Puberty refers to a period of coordinated somatic growth and reproductive maturation that shifts individuals from nonreproductive juvenility to reproductive maturity. Adolescence includes the behavioral and social assumption of adult roles. Life history theory offers powerful tools for understanding why puberty occurs later in humans than in other primates, including the benefits of delayed reproduction as part of a cooperation-intensive life history strategy. It also sheds light on the ways that pubertal timing responds to environmental variation. I review the mechanisms of maturation in humans and propose biocultural approaches to integrate life historical understandings of puberty with a broader definition of environment to encompass the concept of adolescence.
    Print ISSN: 0084-6570
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    Topics: Biology , Ethnic Sciences
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  • 70
    Publication Date: 2019-02-15
    Description: Exosomes are natural nanoparticles that play an important role in cell-to-cell communication. Communication is achieved through the transfer of cargos, such as microRNAs, from donor to recipient cells and binding of exosomes to cell surface receptors. Exosomes and their cargos are also obtained from dietary sources, such as milk. Exosome and cell glycoproteins are crucial for intestinal uptake. A large fraction of milk exosomes accumulates in the brain, whereas the tissue distribution of microRNA cargos varies among distinct species of microRNA. The fraction of milk exosomes that escapes absorption elicits changes in microbial communities in the gut. Dietary depletion of exosomes and their cargos causes a loss of circulating microRNAs and elicits phenotypes such as loss of cognitive performance, increase in purine metabolites, loss of fecundity, and changes in the immune response. Milk exosomes meet the definition of bioactive food compounds.
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  • 71
    Publication Date: 2019-02-15
    Description: One-carbon (1C) metabolism comprises a series of interlinking metabolic pathways that include the methionine and folate cycles that are central to cellular function, providing 1C units (methyl groups) for the synthesis of DNA, polyamines, amino acids, creatine, and phospholipids. S-adenosylmethionine is a potent aminopropyl and methyl donor within these cycles and serves as the principal substrate for methylation of DNA, associated proteins, and RNA. We propose that 1C metabolism functions as a key biochemical conduit between parental environment and epigenetic regulation of early development and that interindividual and ethnic variability in epigenetic-gene regulation arises because of genetic variants within 1C genes, associated epigenetic regulators, and differentially methylated target DNA sequences. We present evidence to support these propositions, drawing upon studies undertaken in humans and animals. We conclude that future studies should assess the epigenetic effects of cumulative (multigenerational) dietary imbalances contemporaneously in both parents, as this better represents the human experience.
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  • 72
    Publication Date: 2019-02-15
    Description: Hepatitis E virus (HEV) is an important human pathogen that historically has been difficult to study. Limited levels of replication in vitro hindered our understanding of the viral life cycle. Sporadic and low-level virus shedding, lack of standardized detection methods, and subclinical infections made the development of animal models difficult. Better diagnostic techniques and understanding of the virus increased our ability to identify and characterize animal strains and animals that are amenable to model human-relevant infection. These advances are translating into the development of useful HEV animal models so that some of the greatest concerns associated with HEV infection, including host immunology, chronic infection, severe pregnancy mortality, and extrahepatic manifestations, can now be studied. Continued development of these animal models will be instrumental in understanding the many complex questions associated with HEV infection and for assessing therapeutics and prevention strategies to minimize HEV becoming a greater risk to the human population.
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  • 73
    Publication Date: 2019-02-15
    Description: The rapid development of aquaculture production throughout the world over the past few decades has led to the emergence of new scientific challenges to improve fish nutrition. The diet formulations used for farmed fish have been largely modified in the past few years. However, bottlenecks still exist in being able to suppress totally marine resources (fish meal and fish oil) in diets without negatively affecting growth performance and flesh quality. A better understanding of fish metabolism and its regulation by nutrients is thus mandatory. In this review, we discuss four fields of research that are highly important for improving fish nutrition in the future: ( a) fish genome complexity and subsequent consequences for metabolism, ( b) microRNAs (miRNAs) as new actors in regulation of fish metabolism, ( c) the role of autophagy in regulation of fish metabolism, and ( d) the nutritional programming of metabolism linked to the early life of fish.
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  • 74
    Publication Date: 2019-06-12
    Description: Sensors are key tools for monitoring the dynamic changes of biomolecules and biofunctions that encode valuable information that helps us understand underlying biological processes of fundamental importance. Because of their distinctive size-dependent physicochemical properties, materials with nanometer scales have recently emerged as promising candidates for biological sensing applications by offering unique insights into real-time changes of key physiological parameters. This review focuses on recent advances in imaging-based nanosensor developments and applications categorized by their signal transduction mechanisms, namely, fluorescence, plasmonics, MRI, and photoacoustics. We further discuss the synergy created by multimodal nanosensors in which sensor components work based on two or more signal transduction mechanisms.
    Print ISSN: 1936-1327
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    Topics: Chemistry and Pharmacology
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  • 75
    Publication Date: 2019-06-12
    Description: Solid-state nanopores and nanopipettes are an exciting class of single-molecule sensors that has grown enormously over the last two decades. They offer a platform for testing fundamental concepts of stochasticity and transport at the nanoscale, for studying single-molecule biophysics and, increasingly, also for new analytical applications and in biomedical sensing. This review covers some fundamental aspects underpinning sensor operation and transport and, at the same time, it aims to put these into context as an analytical technique. It highlights new and recent developments and discusses some of the challenges lying ahead.
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  • 76
    Publication Date: 2019-06-12
    Description: Secreted proteins play important roles in mediating various biological processes such as cell–cell communication, differentiation, migration, and homeostasis at the population or tissue level. Here, we review bioanalytical technologies and devices for detecting protein secretions from single cells. We begin by discussing conventional approaches followed by detailing the latest advances in microengineered systems for detecting single-cell protein secretions with an emphasis on multiplex measurement. These platforms include droplet microfluidics, micro-/nanowell-based assays, and microchamber-based assays, among which the advantages and limitations are compared. Microscale systems also enable the tracking of protein secretion dynamics in single cells, further empowering the study of the cell–cell communication network. Looking forward, we discuss the remaining challenges and future opportunities that will transform basic research of cellular secretion functions at the systems level and the clinical applications for immune monitoring and cancer treatment.
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  • 77
    Publication Date: 2019-06-12
    Description: In the face of looming threats from multi-drug resistant microorganisms, there is a growing need for technologies that will enable rapid identification and drug susceptibility profiling of these pathogens in health care settings. In particular, recent progress in microfluidics and nucleic acid amplification is pushing the boundaries of timescale for diagnosing bacterial infections. With a diverse range of techniques and parallel developments in the field of analytical chemistry, an integrative perspective is needed to understand the significance of these developments. This review examines the scope of new developments in assay technologies grouped by key enabling domains of research. First, we examine recent development in nucleic acid amplification assays for rapid identification and drug susceptibility testing in bacterial infections. Next, we examine advances in microfluidics that facilitate acceleration of diagnostic assays via integration and scale. Lastly, recentdevelopments in biosensor technologies are reviewed. We conclude this review with perspectives on the use of emerging concepts to develop paradigm-changing assays.
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  • 78
    Publication Date: 2019-06-12
    Description: As our ability to synthesize and modify nanoobjects has improved, efforts to explore nanotechnology for diagnostic purposes have gained momentum. The variety of nanoobjects, especially those with polyvalent properties, displays a wide range of practical and unique properties well suited for applications in various diagnostics. This review briefly covers the broad scope of multivalent nanoobjects and their use in diagnostics, ranging from ex vivo assays and biosensors to in vivo imaging. The nanoobjects discussed here include silica nanoparticles, gold nanoparticles, quantum dots, carbon dots, fullerenes, polymers, dendrimers, liposomes, nanowires, and nanotubes. In this review, we describe recent reports of novel applications of these various nanoobjects, particularly as polyvalent entities designed for diagnostics.
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  • 79
    Publication Date: 2019-06-12
    Description: Chromatographic separation has been widely applied in various fields, such as chemical engineering, precision medicine, energy, and biology. Because chromatographic separation is based on differential partitioning between the mobile phase and stationary phase and affected by band dispersion and mass transfer resistance from these two phases, the materials used as the stationary phase play a decisive role in separation performance. In this review, we discuss the design of separation materials to achieve the separation with high efficiency and high resolution and highlight the well-defined materials with uniform pore structure and unique properties. The achievements, recent developments, challenges, and future trends of such materials are discussed. Furthermore, the surface functionalization of separation ma-terials for further improvement of separation performance is reviewed. Finally, future research directions and the challenges of chromatographic separation are presented.
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  • 80
    Publication Date: 2019-03-10
    Description: Complex systems are characterized by many interacting units that give rise to emergent behavior. A particularly advantageous way to study these systems is through the analysis of the networks that encode the interactions among the system constituents. During the past two decades, network science has provided many insights in natural, social, biological, and technological systems. However, real systems are often interconnected, with many interdependencies that are not properly captured by single-layer networks. To account for this source of complexity, a more general framework, in which different networks evolve or interact with each other, is needed. These are known as multilayer networks. Here, we provide an overview of the basic methodology used to describe multilayer systems as well as of some representative dynamical processes that take place on top of them. We round off the review with a summary of several applications in diverse fields of science.
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  • 81
    Publication Date: 2019-03-10
    Description: Contacting bodies subjected to sufficiently large applied shear will undergo frictional sliding. The onset of this motion is mediated by dynamically propagating fronts, akin to earthquakes, that rupture the discrete contacts that form the interface separating the bodies. Macroscopic motion commences only after these ruptures have traversed the entire interface. Comparison of measured rupture dynamics with the detailed predictions of fracture mechanics reveals that the propagation dynamics, dissipative properties, radiation, and arrest of these “laboratory earthquakes” are in excellent quantitative agreement with the predictions of the theory of brittle fracture. Thus, interface fracture replaces the idea of a characteristic static friction coefficient as a description of the onset of friction. This fracture-based description of friction additionally provides a fundamental description of earthquake dynamics and arrest.
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  • 82
    Publication Date: 2019-03-10
    Description: Superfluid 3He is an unconventional neutral superfluid in a p-wave state with three different superfluid phases, each identified by a unique set of characteristic broken symmetries and nontrivial topology. Despite natural immunity of 3He from defects and impurity of any kind, it has been found that they can be artificially introduced with high-porosity silica aerogel. Furthermore, it has been shown that this modified quantum liquid becomes a superfluid with remarkably sharp thermodynamic transitions from the normal state and between its various phases. These phases include new superfluid phases that are stabilized by anisotropy from uniform strain imposed on the silica aerogel framework, and they include new phenomena in a new class of anisotropic aerogels consisting of nematically ordered alumina strands. The study of superfluid 3He in the presence of correlated, quenched disorder from aerogel serves as a model for understanding the effect of impurities on the symmetry and topology of unconventional superconductors.
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  • 83
    Publication Date: 2019-03-10
    Description: This article focuses on the history of theoretical ideas but also on the developments of experimental tools. The experiments in our laboratory are used to illustrate the various developments associated with Brownian movement. In the first part of this review, we give an overview of the theory. We insist on the pre-Einstein approach to the problem by Lord Rayleigh, Bachelier, and Smoluchowski. In the second part, we detail the achievements of Perrin, measuring Avogadro's number, quantifying the experimental observations of Brownian movement, and introducing the problem of continuous curves without tangent, a precursor to fractal theory. The third part deals with modern application of Brownian movement, escape from a fixed optical trap, particle dynamics on a moving trap, and finally development of Brownian thermal ratchets. Finally, we give a short overview of bacteria motion, presented like an active Brownian movement with very high effective temperature.
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  • 84
    Publication Date: 2019-06-20
    Description: The centriole is an ancient microtubule-based organelle with a conserved nine-fold symmetry. Centrioles form the core of centrosomes, which organize the interphase microtubule cytoskeleton of most animal cells and form the poles of the mitotic spindle. Centrioles can also be modified to form basal bodies, which template the formation of cilia and play central roles in cellular signaling, fluid movement, and locomotion. In this review, we discuss developments in our understanding of the biogenesis of centrioles and cilia and the regulatory controls that govern their structure and number. We also discuss how defects in these processes contribute to a spectrum of human diseases and how new technologies have expanded our understanding of centriole and cilium biology, revealing exciting avenues for future exploration.
    Print ISSN: 0066-4154
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    Topics: Biology , Chemistry and Pharmacology
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  • 85
    Publication Date: 2019-06-20
    Description: Botulinum neurotoxins (BoNTs) and tetanus neurotoxin (TeNT) are the most potent toxins known and cause botulism and tetanus, respectively. BoNTs are also widely utilized as therapeutic toxins. They contain three functional domains responsible for receptor-binding, membrane translocation, and proteolytic cleavage of host proteins required for synaptic vesicle exocytosis. These toxins also have distinct features: BoNTs exist within a progenitor toxin complex (PTC), which protects the toxin and facilitates its absorption in the gastrointestinal tract, whereas TeNT is uniquely transported retrogradely within motor neurons. Our increasing knowledge of these toxins has allowed the development of engineered toxins for medical uses. The discovery of new BoNTs and BoNT-like proteins provides additional tools to understand the evolution of the toxins and to engineer toxin-based therapeutics. This review summarizes the progress on our understanding of BoNTs and TeNT, focusing on the PTC, receptor recognition, new BoNT-like toxins, and therapeutic toxin engineering.
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  • 86
    Publication Date: 2019-06-20
    Description: The stage at which ribosomes are recruited to messenger RNAs (mRNAs) is an elaborate and highly regulated phase of protein synthesis. Upon completion of this step, a ribosome is positioned at an appropriate initiation codon and primed to synthesize the encoded polypeptide product. In most circumstances, this step commits the ribosome to translate the mRNA. We summarize the knowledge regarding the initiation factors implicated in this activity as well as review different mechanisms by which this process is conducted.
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  • 87
    Publication Date: 2019-06-20
    Description: The timely production of functional proteins is of critical importance for the biological activity of cells. To reach the functional state, newly synthesized polypeptides have to become enzymatically processed, folded, and assembled into oligomeric complexes and, for noncytosolic proteins, translocated across membranes. Key activities of these processes occur cotranslationally, assisted by a network of machineries that transiently engage nascent polypeptides at distinct phases of translation. The sequence of events is tuned by intrinsic features of the nascent polypeptides and timely association of factors with the translating ribosome. Considering the dynamics of translation, the heterogeneity of cellular proteins, and the diversity of interaction partners, it is a major cellular achievement that these processes are temporally and spatially so precisely coordinated, minimizing the generation of damaged proteins. This review summarizes the current progress we have made toward a comprehensive understanding of the cotranslational interactions of nascent chains, which pave the way to their functional state.
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  • 88
    Publication Date: 2019-06-20
    Description: Genomic DNA is susceptible to endogenous and environmental stresses that modify DNA structure and its coding potential. Correspondingly, cells have evolved intricate DNA repair systems to deter changes to their genetic material. Base excision DNA repair involves a number of enzymes and protein cofactors that hasten repair of damaged DNA bases. Recent advances have identified macromolecular complexes that assemble at the DNA lesion and mediate repair. The repair of base lesions generally requires five enzymatic activities: glycosylase, endonuclease, lyase, polymerase, and ligase. The protein cofactors and mechanisms for coordinating the sequential enzymatic steps of repair are being revealed through a range of experimental approaches. We discuss the enzymes and protein cofactors involved in eukaryotic base excision repair, emphasizing the challenge of integrating findings from multiple methodologies. The results provide an opportunity to assimilate biochemical findings with cell-based assays to uncover new insights into this deceptively complex repair pathway.
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  • 89
    Publication Date: 2019-06-20
    Description: Antibodies are immunoglobulins that play essential roles in immune systems. All antibodies are glycoproteins that carry at least one or more conserved N-linked oligosaccharides ( N-glycans) at the Fc domain. Many studies have demonstrated that both the presence and fine structures of the attached glycans can exert a profound impact on the biological functions and therapeutic efficacy of antibodies. However, antibodies usually exist as mixtures of heterogeneous glycoforms that are difficult to separate in pure glycoforms. Recent progress in glycoengineering has provided useful methods that enable production of glycan-defined and site-selectively modified antibodies for functional studies and for improved therapeutic efficacy. This review highlights major approaches in glycoengineering of antibodies with a focus on recent advances in three areas: glycoengineering through glycan biosynthetic pathway manipulation, glycoengineering through in vitro chemoenzymatic glycan remodeling, and glycoengineering of antibodies for site-specific antibody–drug conjugation.
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  • 90
    Publication Date: 2019-10-06
    Description: Many cellular processes rely on precise and timely deformation of the cell membrane. While many proteins participate in membrane reshaping and scission, usually in highly specialized ways, Bin/amphiphysin/Rvs (BAR) domain proteins play a pervasive role, as they not only participate in many aspects of cell trafficking but also are highly versatile membrane remodelers. Subtle changes in the shape and size of the BAR domain can greatly impact the way in which BAR domain proteins interact with the membrane. Furthermore, the activity of BAR domain proteins can be tuned by external physical parameters, and so they behave differently depending on protein surface density, membrane tension, or membrane shape. These proteins can form 3D structures that mold the membrane and alter its liquid properties, even promoting scission under various circumstances.As such, BAR domain proteins have numerous roles within the cell. Endocytosis is among the most highly studied processes in which BAR domain proteins take on important roles. Over the years, a more complete picture has emerged in which BAR domain proteins are tied to almost all intracellular compartments; examples include endosomal sorting and tubular networks in the endoplasmic reticulum and T-tubules. These proteins also have a role in autophagy, and their activity has been linked with cancer. Here, we briefly review the history of BAR domain protein discovery, discuss the mechanisms by which BAR domain proteins induce curvature, and attempt to settle important controversies in the field. Finally, we review BAR domain proteins in the context of a cell, highlighting their emerging roles in cell signaling and organelle shaping.
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    Electronic ISSN: 1530-8995
    Topics: Biology , Medicine
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  • 91
    Publication Date: 2019-10-06
    Description: Autophagy is the major cellular pathway to degrade dysfunctional organelles and protein aggregates. Autophagy is particularly important in neurons, which are terminally differentiated cells that must last the lifetime of the organism. There are both constitutive and stress-induced pathways for autophagy in neurons, which catalyze the turnover of aged or damaged mitochondria, endoplasmic reticulum, other cellular organelles, and aggregated proteins. These pathways are required in neurodevelopment as well as in the maintenance of neuronal homeostasis. Here we review the core components of the pathway for autophagosome biogenesis, as well as the cell biology of bulk and selective autophagy in neurons. Finally, we discuss the role of autophagy in neuronal development, homeostasis, and aging and the links between deficits in autophagy and neurodegeneration.
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  • 92
    Publication Date: 2019-03-10
    Description: A hallmark of the phase diagrams of quantum materials is the existence of multiple electronic ordered states, which, in many cases, are not independent competing phases, but instead display a complex intertwinement. In this review, we focus on a particular realization of intertwined orders: a primary phase characterized by a multi-component order parameter and a fluctuation-driven vestigial phase characterized by a composite order parameter. This concept has been widely employed to elucidate nematicity in iron-based and cuprate superconductors. Here we present a group-theoretical framework that extends this notion to a variety of phases, providing a classification of vestigial orders of unconventional superconductors and density waves. Electronic states with scalar and vector chiral order, spin-nematic order, Ising-nematic order, time-reversal symmetry-breaking order, and algebraic vestigial order emerge from one underlying principle. The formalism provides a framework to understand the complexity of quantum materials based on symmetry, largely without resorting to microscopic models.
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  • 93
    Publication Date: 2019-03-10
    Description: Fracton phases constitute a new class of quantum state of matter. They are characterized by excitations that exhibit restricted mobility, being either immobile under local Hamiltonian dynamics or mobile only in certain directions. These phases do not wholly fit into any of the existing paradigms but connect to areas including glassy quantum dynamics, topological order, spin liquids, elasticity theory, quantum information theory, and gravity. We begin by discussing gapped fracton phases, which may be described using exactly solvable lattice spin models. We then introduce the framework of tensor gauge theory, which provides a powerful complementary perspective and allows us to access gapless fracton phases. We discuss the basic properties of gapless fracton phases and their connections to elasticity theory and gravity. We also discuss what is known about the dynamics and thermodynamics of fractons at nonzero density before concluding with a brief survey of some open problems.
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  • 94
    Publication Date: 2019-03-10
    Description: In this review, we provide an introduction to the physics of a series of frustrated quantum rare-earth pyrochlores. We first give a background on the microscopic single- and two-ion physics of these materials, discussing the origins and properties of their exchange interactions and their minimal low-energy effective models before outlining what is known about their classical and quantum phases. We then make use of this understanding to discuss four important material examples, Er2Ti2O7, Yb2Ti2O7, Tb2Ti2O7, and Pr2Zr2O7, covering in some detail what is known experimentally and theoretically for each and then summarizing some key questions that remain open. Finally, we offer an outlook on some alternative material platforms for realizing similar physics and discuss what we see as prospects for future investigations on these quantum rare-earth pyrochlores.
    Print ISSN: 1947-5454
    Electronic ISSN: 1947-5462
    Topics: Physics
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  • 95
    Publication Date: 2019-03-10
    Description: Soft-condensed matter physics has provided, in the past decades, many of the relevant concepts and methods allowing successful description of living cells and biological tissues. This recent quantitative physical description of biological systems has profoundly advanced our understanding of life, which is shifting from a descriptive to a predictive level. Like other active materials investigated in condensed matter physics, biological materials still pose great challenges to modern physics as they form a specific class of nonequilibrium systems. Actively driven membranes have been studied for more than two decades, taking advantage of rapid progress in membrane physics and in the experimental development of reconstituted active membranes. The physical description of activity within living biological membranes remains, however, a key challenge that animates a dynamic research community, bringing together physicists and biologists. Here, we first review the past two decades of experimental and theoretical advances that enabled the characterization of mechanical properties and nonequilibrium fluctuations in active membranes. We distinguish active processes originating from membrane proteins or from external interactions, such as cytoskeletal forces. Then, we focus on the emblematic case of red blood cell flickering, the active origin of which has been debated for decades until recently. We finally close this review by discussing future challenges in this ever more interdisciplinary field.
    Print ISSN: 1947-5454
    Electronic ISSN: 1947-5462
    Topics: Physics
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  • 96
    Publication Date: 2019-03-10
    Description: Strontium titanate is a wide-gap semiconductor avoiding a ferroelectric instability thanks to quantum fluctuations. This proximity leads to strong screening of static Coulomb interaction and paves the way for the emergence of a very dilute metal with extremely mobile carriers at liquid-helium temperature. Upon warming, mobility decreases by several orders of magnitude. Yet, metallicity persists above room temperature even when the apparent mean free path falls below the electron wavelength. The superconducting instability survives at exceptionally low concentrations and beyond the boundaries of Migdal–Eliashberg approximation. An intimate connection between dilute superconductivity and aborted ferroelectricity is widely suspected. In this review, we give a brief account of ongoing research on bulk strontium titanate as an insulator, a metal, and a superconductor.
    Print ISSN: 1947-5454
    Electronic ISSN: 1947-5462
    Topics: Physics
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  • 97
    Publication Date: 2019-03-10
    Description: Metallic quantum critical phenomena are believed to play a key role in many strongly correlated materials, including high-temperature superconductors. Theoretically, the problem of quantum criticality in the presence of a Fermi surface has proven to be highly challenging. However, it has recently been realized that many models used to describe such systems are amenable to numerically exact solution by quantum Monte Carlo (QMC) techniques, without suffering from the fermion sign problem. In this review, we examine the status of the understanding of metallic quantum criticality and the recent progress made by QMC simulations. We focus on the cases of spin-density wave and Ising nematic criticality. We describe the results obtained so far and their implications for superconductivity, non-Fermi liquid behavior, and transport near metallic quantum critical points. Some of the outstanding puzzles and future directions are highlighted.
    Print ISSN: 1947-5454
    Electronic ISSN: 1947-5462
    Topics: Physics
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  • 98
    Publication Date: 2019-03-10
    Description: Spin liquids are collective phases of quantum matter that have eluded discovery in correlated magnetic materials for over half a century. Theoretical models of these enigmatic topological phases are no longer in short supply. In experiment there also exist plenty of promising candidate materials for their realization. One of the central challenges for the clear diagnosis of a spin liquid has been to connect the two. From that perspective, this review discusses characteristic features in experiment, resulting from the unusual properties of spin liquids. This takes us to thermodynamic, spectroscopic, transport, and other experiments on a search for traces of emergent gauge fields, spinons, Majorana fermions, and other fractionalized particles.
    Print ISSN: 1947-5454
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    Topics: Physics
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  • 99
    Publication Date: 2019-03-10
    Description: Many objects in nature and industry are wrapped in a thin sheet to enhance their chemical, mechanical, or optical properties. Similarly, there are a variety of methods for wrapping, from pressing a film onto a hard substrate to inflating a closed membrane, to spontaneously wrapping droplets using capillary forces. Each of these settings raises challenging nonlinear problems involving the geometry and mechanics of a thin sheet, often in the context of resolving a geometric incompatibility between two surfaces. Here, we review recent progress in this area, focusing on highly bendable films that are nonetheless hard to stretch, a class of materials that includes polymer films, metal foils, textiles, and graphene, as well as some biological materials. Significant attention is paid to two recent advances: a novel isometry that arises in the doubly-asymptotic limit of high flexibility and weak tensile forcing, and a simple geometric model for predicting the overall shape of an interfacial film while ignoring small-scale wrinkles, crumples, and folds.
    Print ISSN: 1947-5454
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    Topics: Physics
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  • 100
    Publication Date: 2019-03-10
    Description: Reliable simulations of correlated quantum systems, including high-temperature superconductors and frustrated magnets, are increasingly desired nowadays to further our understanding of essential features in such systems. Quantum Monte Carlo (QMC) is a unique numerically exact and intrinsically unbiased method to simulate interacting quantum many-body systems. More importantly, when QMC simulations are free from the notorious fermion sign problem, they can reliably simulate interacting quantum models with large system size and low temperature to reveal low-energy physics such as spontaneously broken symmetries and universal quantum critical behaviors. Here, we concisely review recent progress made in developing new sign-problem-free QMC algorithms, including those employing Majorana representation and those utilizing hot-spot physics. We also discuss applications of these novel sign-problem-free QMC algorithms in simulations of various interesting quantum many-body models. Finally, we discuss possible future directions of designing sign-problem-free QMC methods.
    Print ISSN: 1947-5454
    Electronic ISSN: 1947-5462
    Topics: Physics
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